From 747b87d3ec82b787c26c7ad95975e787ab7e1a72 Mon Sep 17 00:00:00 2001
From: John Marshall <john.marshall@populationgenomics.org.au>
Date: Wed, 25 Sep 2024 10:41:20 +1200
Subject: [PATCH] [batch] Ignore empty command strings when constructing shell
 scripts

Using job.command('') (or more likely something more complex
that sometimes evaluates to an empty string) led to shell snippets
containing `... { } ...`, which is a shell syntax error. Prevent
this by not adding such strings to self._command and warning.
---
 hail/python/hailtop/batch/job.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/hail/python/hailtop/batch/job.py b/hail/python/hailtop/batch/job.py
index 97eb45be0d4..facf34f1e2c 100644
--- a/hail/python/hailtop/batch/job.py
+++ b/hail/python/hailtop/batch/job.py
@@ -859,6 +859,11 @@ def command(self, command: str) -> 'BashJob':
         Same job object with command appended.
         """
 
+        if command.strip() == '':
+            job_name = f'job {self.name!r}' if self.name else 'unnamed job'
+            warnings.warn(f'Ignoring empty command specified for {job_name}.')
+            return self
+
         command = self._interpolate_command(command)
         self._command.append(command)
         return self